Releases | Open Source Science

variation-normalization - 0.15.0

What's Changed

feat!: add input assembly parameter for free text genomic / gnomad vcf queries by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/619

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/0.14.2...0.15.0

- Python
Published by korikuzma 6 months ago

variation-normalization - 0.14.2

What's Changed

feat: add docker install instructions by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/613
style: update ruff and precommit by @jsstevenson in https://github.com/cancervariants/variation-normalization/pull/614
build: tighten ga4gh.vrs + cool-seq-tool versions by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/615
docs: fix previous vrs version table by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/616
feat: expose cool-seq-tool feature overlap endpoint by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/618

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/0.14.1...0.14.2

- Python
Published by korikuzma 6 months ago

variation-normalization - 0.14.1

What's Changed

build: bump cool-seq-tool version (#611) by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/612

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/0.14.0...0.14.1

- Python
Published by korikuzma 9 months ago

variation-normalization - 0.14.0

What's Changed

build!: update ga4gh.vrs by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/597
revert(ci): revert back to using ubuntu-latest in gh action test job by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/598
Migrate staging changes into main by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/599
cicd: update ruff and precommit checks by @jsstevenson in https://github.com/cancervariants/variation-normalization/pull/600
chore: update seqrepo version to 2024-12-20 by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/604
docs: update uta version to 20241220 by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/605
chore: update developer installation for uta by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/603
build!: update cool-seq-tool version by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/606
feat!: update to vrs 2.0.1 models by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/608

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/0.12.2...0.14.0

- Python
Published by korikuzma 9 months ago

variation-normalization - 0.13.0

What's Changed

build!: update ga4gh.vrs by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/597
revert(ci): revert back to using ubuntu-latest in gh action test job by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/598

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/0.12.2..0.13.0

- Python
Published by korikuzma 11 months ago

variation-normalization - 0.12.2

What's Changed

build: update cool-seq-tool + pin gene-normalizer by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/596

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/0.12.1...0.12.2

- Python
Published by korikuzma 11 months ago

variation-normalization - 0.12.1

What's Changed

build: pin gene-normalizer version to >=0.7.0 by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/595

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/0.12.0...0.12.1

- Python
Published by korikuzma 11 months ago

variation-normalization - 0.12.0

What's Changed

build: pin cool-seq-tool version ~=0.9.1 by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/589
feat!: rename residue mode to coordinate type by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/591
build: update cool-seq-tool version in Pipfile by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/592

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/0.11.0...0.12.0

- Python
Published by korikuzma 12 months ago

variation-normalization - 0.11.0

What's Changed

build: pin cool-seq-tool~=0.6.0 by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/575
feat: return MANE gene(s) in normalize endpoint for genomic queries by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/576
cicd: check if PR to main is coming from staging by @jsstevenson in https://github.com/cancervariants/variation-normalization/pull/580
chore!: rename optional dependency by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/583
feat!: update models to vrs 2.0.0 community review ballot by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/582
build!: require python >= 3.11 by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/586
docs: update readme with vrs versioning by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/585
fix(build): update dependency versions in Pipfile by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/584

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/0.10.0...0.11.0

- Python
Published by korikuzma 12 months ago

variation-normalization - 0.10.0

What's Changed

cicd: allow missing credentials in aws creds detection by @jsstevenson in https://github.com/cancervariants/variation-normalization/pull/569
feat!: add sequence to SequenceLocation by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/570
fix: update ga4gh.vrs + add back response_model configs for FastAPI by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/571
docs: update vrs versioning by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/572

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/0.9.1...0.10.0

- Python
Published by korikuzma over 1 year ago

variation-normalization - 0.9.1

What's Changed

fix: version imports by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/565
chore: remove unused files by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/568
style: ruff format by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/567
fix: TypeError for params that accept union of enums by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/566
chore: update ebextensions for downloading latest seqrepo instance by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/564

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/0.9.0...0.9.1

- Python
Published by korikuzma over 1 year ago

variation-normalization - 0.9.0

What's Changed

build: reorganize build metadata (#549) by @jsstevenson in https://github.com/cancervariants/variation-normalization/pull/550
chore: update license by @jsstevenson in https://github.com/cancervariants/variation-normalization/pull/547
cicd: require priority label on PRs by @jsstevenson in https://github.com/cancervariants/variation-normalization/pull/546
cicd: test install on 3.12 by @jsstevenson in https://github.com/cancervariants/variation-normalization/pull/544
docs: readme glow-up by @jsstevenson in https://github.com/cancervariants/variation-normalization/pull/548
cicd: update precommit by @jsstevenson in https://github.com/cancervariants/variation-normalization/pull/558
cicd: update workflows/templates from template repo by @jsstevenson in https://github.com/cancervariants/variation-normalization/pull/556
feat: enable more precise logging configuration by @jsstevenson in https://github.com/cancervariants/variation-normalization/pull/559
cicd: update precommit dependency in pipfile by @jsstevenson in https://github.com/cancervariants/variation-normalization/pull/560
style: update ruff by @jsstevenson in https://github.com/cancervariants/variation-normalization/pull/557
build!: update ga4gh.vrs, cool-seq-tool, + gene-normalizer by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/561
build: update requirements and build system by @jsstevenson in https://github.com/cancervariants/variation-normalization/pull/555
docs: update seqrepo version to 2024-02-20 by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/562
fix(cicd): add reference to stalebot by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/563

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/0.8.2...0.9.0

- Python
Published by korikuzma over 1 year ago

variation-normalization - 0.8.2

What's Changed

test: only check vrs ids on certain tests by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/540
build!: udpate ga4gh.vrs version by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/542

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/0.8.1...0.8.2

- Python
Published by korikuzma almost 2 years ago

variation-normalization - 0.8.1

What's Changed

build: pin ga4gh.vrs dependency by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/539

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/0.8.1-dev0...0.8.1

- Python
Published by korikuzma almost 2 years ago

variation-normalization - 0.8.1-dev0

What's Changed

feat!: add more support for queries in gnomadvcfto_protein by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/529
style: replace black with ruff by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/532
build: modernize build configs by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/533
fix: handle cases where gene_context is not found by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/536
cicd: fix elastic beanstalk deployment by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/537

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/0.8.0-dev1...0.8.1-dev0

- Python
Published by korikuzma almost 2 years ago

variation-normalization - 0.8.0-dev1

What's Changed

fix: hgvs/free text dup/del end positions for definite ranges by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/525
build!: update cool-seq-tool + ga4gh.vrs versions by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/528
- Temporarily removes gnomadvcfto_protein

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/0.8.0-dev0...0.8.0-dev1

- Python
Published by korikuzma almost 2 years ago

variation-normalization - 0.6.0-dev1

What's Changed

cicd: update release.yml (publish python distribution to pypi) by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/513
fix: pin versions + fix /translate_identifier by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/516
feat: expose cool-seq-tool feature overlap endpoint by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/523

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/0.6.0-dev0...0.6.0-dev1

- Python
Published by korikuzma about 2 years ago

variation-normalization - 0.8.0-dev0

What's Changed

fix: catch errors for (#_#)_#dup and #_(#_#)dup HGVS exprs by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/419
docs: document branch / version tracking by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/403
ci: add GH action for installing deps + remove requirements (metaschema) by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/452
chore: update elastic beanstalk commands by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/456
feat: add parsed to copy number change endpoint (metaschema) by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/453
fix!: /parsed_to_cn_var should accept number, definite range, and indefinite range by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/455
feat: add do_liftover param in parsed to copy number endpoints (metaschema) by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/459
refactor!: parsed to copy number should accept request body (metaschema) by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/460
build: update ga4gh.vrsatile.pydantic version by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/461
fix: Copy Number Count copies should be Number or Indef/Def Range by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/468
fix: allow comparator to be set in start/end values by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/469
refactor!: clean up app (metaschema) by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/494
feat!: update to vrs 2.0-alpha by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/512
cicd: update release.yml (publish python distribution to pypi) by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/514
build!: update depdency versions by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/517
fix: vrs-python translator import statement by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/520

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/0.7.0-dev7...0.8.0-dev0

- Python
Published by korikuzma about 2 years ago

variation-normalization - 0.6.0-dev0

What's Changed

analysis: civic + moa variant analysis by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/439
ci: add GH action for installing deps + remove requirements by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/442
revert: analysis: civic + moa variant analysis (#439) by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/446
build: update ga4gh.vrsatile.pydantic version by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/462
cicd: update scproductid by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/472
refactor! by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/503

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/0.5.5...0.6.0-dev0

- Python
Published by korikuzma over 2 years ago

variation-normalization - 0.5.5

What's Changed

build: bump gene-normalizer version to 0.1.36 by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/421
fix: catch errors for (##)#dup and #(##)dup HGVS exprs (#419) by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/422
docs: update query descriptions for /to_vrs and /normalize by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/423
docs: document branch / version tracking (#403) by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/424

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/0.5.4...0.5.5

- Python
Published by korikuzma over 2 years ago

variation-normalization - 0.5.4

What's Changed

refactor: Allow option to use existing gene-normalizer instance by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/396
refactor!: initial cleanup of tokenizers by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/395
feat!: Apply VRS 1.3 Changes by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/409

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/0.5.3...0.5.4

- Python
Published by korikuzma over 2 years ago

variation-normalization - 0.7.0-dev7

What's Changed

fix: update cool-seq-tool to 0.1.13 by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/410

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/0.7.0-dev6...0.7.0-dev7

- Python
Published by korikuzma over 2 years ago

variation-normalization - 0.7.0-dev6

What's Changed

Issue 394 metaschema by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/402

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/0.7.0-dev5...0.7.0-dev6

- Python
Published by korikuzma over 2 years ago

variation-normalization - 0.7.0-dev5

What's Changed

refactor: Allow option to use existing gene-normalizer instance (staging) by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/397
refactor!: initial cleanup of tokenizers (metaschema-update) by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/399

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/0.7.0-dev4...0.7.0-dev5

- Python
Published by korikuzma over 2 years ago

variation-normalization - 0.7.0-dev4

What's Changed

ci: resolve actions version warnings by @jsstevenson in https://github.com/cancervariants/variation-normalization/pull/335
build: update gene-normalizer version to v0.2.6 (staging) by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/337
build!: replace uta tools with cool seq tool (dev) by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/341
change: relativecopyclass uses EFO IDs by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/346
build: update dependency versions by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/352
perf: gnomadvcfto_protein replace call to uta db with df lookup (staging) by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/353
build: update dependencies (staging) by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/376
fix: TypeError in isgrch38_assembly (stgaging) by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/375
cicd: revert dev termination time back to 12 hours by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/377
fix: remove duplicate warnings in gnomadvcfto_protein (staging) by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/382
refactor: replace AminoAcidCache with bioutils (staging) by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/381
fix: add support for ambiguous N IUPAC code for cDNA + genomic (staging) by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/384
refactor!: update cool-seq-tool (staging) by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/392
feat: add support for amino acids after del (staging) by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/393

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/v0.7.dev0...0.7.0-dev4

- Python
Published by korikuzma over 2 years ago

variation-normalization - 0.5.3

What's Changed

refactor: replace AminoAcidCache with bioutils by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/366
feat: add support for amplification queries (main) by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/367
build(deps): bump starlette from 0.22.0 to 0.25.0 by @dependabot in https://github.com/cancervariants/variation-normalization/pull/371
build(deps): bump ipython from 8.9.0 to 8.10.0 by @dependabot in https://github.com/cancervariants/variation-normalization/pull/370
build: update dependencies by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/373
fix: TypeError in isgrch38_assembly by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/374
feat: expose cool-seq-tool alignment mapper endpoints by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/380
fix: add support for ambiguous N IUPAC code for cDNA + genomic by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/385
feat: add support for amino acids after del by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/386
refactor!: update cool-seq-tool by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/391

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/v0.5.2...0.5.3

- Python
Published by korikuzma over 2 years ago

variation-normalization - v0.5.2

What's Changed

build!: replace uta tools with cool seq tool by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/340
perf: gnomad vcf -> p will try mane transcript result first by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/343
perf: gnomadvcfto_protein replace call to uta db with df lookup (main) by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/350
build: unpin ga4gh.vrs + bump gene-normalizer (main) by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/351
change: version by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/354
fix: remove duplicate warnings in gnomadvcfto_protein by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/356

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/v0.5.1...v0.5.2

- Python
Published by korikuzma almost 3 years ago

variation-normalization - v0.5.1

What's Changed

Bump lxml from 4.9.0 to 4.9.1 by @dependabot in https://github.com/cancervariants/variation-normalization/pull/305
BREAKING CHANGE: refactor: simplify QueryHandler class by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/304
docs: update readme for setting up backend services by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/306
refactor!: main query methods return pydantic service class response by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/308
refactor: update route descriptions by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/312
refactor: service response by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/316
build: update gene-normalizer to v.1.30 by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/338

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/v0.4.0a7...v0.5.1

- Python
Published by korikuzma about 3 years ago

variation-normalization - v0.7.dev0

What's Changed

feat: add support for amplification queries by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/333

Full Changelog: https://github.com/cancervariants/variation-normalization/compare/v0.6.3...v0.7.dev0

- Python
Published by korikuzma over 3 years ago

variation-normalization -

build: update uta tools + other dependencies
fix: gnomadvcfto_protein getting ref/alt values

- Python
Published by korikuzma over 3 years ago

variation-normalization -

feat: add endpoint for vrs-python tohgvs method

- Python
Published by korikuzma over 3 years ago

variation-normalization -

Switch request body for /translate_to to use pydantic.BaseModel so users can test out the endpoint on the UI

- Python
Published by korikuzma over 3 years ago

variation-normalization -

Add endpoint (/translate_to) for vrs-python's translate_to method

- Python
Published by korikuzma over 3 years ago

variation-normalization -

Add parsed_to_abs_cnv endpoint to allow parsed ClinVar Copy Number Gain/Loss to be translated to VRS Absolute Copy Number variation

- Python
Published by korikuzma over 3 years ago

variation-normalization -

Adds relative_cnv option to hgvs_dup_del_mode
- Default characteristics for HGVS Dup Del Mode updated
/tocanonicalvariation parameters added
- do_liftover: Whether or not to liftover 37 to 38
- hgvs_dup_del_mode: Set to determine the VRS variation model used
  - baseline_copies is required when hgvs_dup_del_mode=absolute_cnv
  - relative_copy_class is optional when hgvs_dup_del_mode=relative_cnv

- Python
Published by korikuzma over 3 years ago

variation-normalization -

CNVs use SequenceLocation as the subject
/toVRS --> /to_vrs
Add fastapi tags
Add initial /tocanonicalvariation endpoint for HGVS/SPDI

- Python
Published by korikuzma over 3 years ago

variation-normalization -

HGVS to relative / absolute copy number endpoints
Remove unused methods from validator (human / concise description)
Use uta-tools to handle MANE transcript work

- Python
Published by korikuzma over 3 years ago

variation-normalization -

Bump jupyter-server from 1.13.5 to 1.15.4

- Python
Published by korikuzma almost 4 years ago

variation-normalization -

Add vrs-python's translate_from method (hgvs/spdi/beacon/gnomad --> VRS Allele object)

- Python
Published by korikuzma almost 4 years ago

variation-normalization -

Adds dockerfile
Set variation descriptor's label to input query
Replace pandas.read_sql in uta data source
Add canonical spdi to categorical variation endpoint

- Python
Published by korikuzma almost 4 years ago

variation-normalization -

Remove normalized MANE Transcript response from toVRS

- Python
Published by korikuzma almost 4 years ago

variation-normalization -

Removes unused hgvs.parser from validator + mane transcript
Fix bug in deletions state

- Python
Published by korikuzma almost 4 years ago

variation-normalization -

Add url to openapi contact info
Always enable Try it out param in FastAPI
Add citation
Update dependencies
- sqlalchemy
- psycopg2-binary (dev)

- Python
Published by korikuzma almost 4 years ago

variation-normalization - VICC Variation Normalization

The January 2022 pre-release of the VICC variation normalization software, live instance available online at http://normalize.cancervariants.org/variation

- Python
Published by ahwagner almost 4 years ago

variation-normalization -

Catches ValueError when creating a sequence location whose namespace can't be inferred

- Python
Published by korikuzma about 4 years ago

variation-normalization -

Add translate_identifier endpoint
Fix bug in UTA for ordering alt_ac by desc
Add support for basic gnomad VCF substitution, insertion, and deletion
Add support for gnomad VCF -> MANE p

- Python
Published by korikuzma about 4 years ago

variation-normalization -

Add HGVS Del Dup Mode in normalize endpoint
- Currently only supports genomic deletions and duplications
Update to VRS 1.2.0 models
Add _id in all VRS models
Fix position bug in MANE transcript

- Python
Published by korikuzma about 4 years ago

variation-normalization -

Only get MANE Transcript if gene is provided in genomic queries
SEQREPODATAPATH uses /usr/local/share/seqrepo/latest path
Use latest gene-normalizer

- Python
Published by korikuzma about 4 years ago